MmuINT0141129 @ mm9
Intron Retention
Gene
ENSMUSG00000026121 | Sema4c
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:MGI Symbol;Acc:MGI:109252]
Coordinates
chr1:36608772-36609241:-
Coord C1 exon
chr1:36609097-36609241
Coord A exon
chr1:36608995-36609096
Coord C2 exon
chr1:36608772-36608994
Length
102 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CACGCCCCTCCCCGACACAGTGT
3' ss Score
6.03
Exon sequences
Seq C1 exon
GGGCGATATGGACCTGTCTGCAGTTTGTGAGTACCAGTTGGAACAGATCCAGCAAGTGTTTGAGGGTCCCTACAAGGAGTACAGTGAGCAAGCCCAGAAGTGGGCCCGCTATACTGACCCGGTACCCAGCCCTCGGCCTGGTTCG
Seq A exon
GTGAGTTTTCGGCTTGGGGATGTATTCCCAACATCGGCTCCAGGACCCACTTATTCGCCAGCTGACTGACAGCCGCCCTCCCCACGCCCCTCCCCGACACAG
Seq C2 exon
TGTATCAACAACTGGCACCGAGACAATGGCTACACCAGTTCCCTGGAACTGCCGGACAACACCCTCAACTTCATCAAGAAGCACCCCCTGATGGAGGACCAGGTGAAGCCTCGGTTGGGCCGCCCCCTACTTGTGAAGAAGAACACTAACTTCACACACGTGGTGGCCGACAGGGTCCCAGGGCTTGATGGTGCCACCTATACAGTGTTGTTCATTGGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026121-Sema4c:NM_001126047:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.013
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.2=100)
A:
NA
C2:
PF0140314=Sema=FE(17.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGATATGGACCTGTCTGCAG
R:
GCTTCACCTGGTCCTCCATCA
Band lengths:
252-354
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: